I'm running Subsonic on a Synology NAS. Their system will create @eaDir folders all over the place in a network share to store "extended attributes". These folders contain metadata files with the same names as the actual music files.
Subsonic now lists every song twice in it's search index (one of them not being a valid song), and also displays the @eaDir folders in the GUI.
I suggest that the to ignore @eaDir folders on all platforms is a good enough solution; alternatively, an option could be provided to allow for custom ignores.
See also here: http://forum.subsonic.org/forum/viewtopic.php?p=25285